Dear Justin,<br><br>I am using the commands as the following.<br>do_dssp -s run.tpr -f run.xtc<br>xpm2ps -f ss.xpm -o ss.eps<br><br>You said "Have a look at the other output file do_dssp gives you". <span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">which one</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">should I look?<br>
<br>Thanks<br><br></span></span><div class="gmail_quote">04 Ocak 2011 15:51 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I get the residue versus time ( secondary structure graph) using do_dssp tool. I want to get the percentage value(alpha helix, beta sheet, coil ...) of secondary structure. For example:<br>
<br>
Secondary structure percentage (%):<br>
Helix:51.6<br>
B-sheet:0<br>
Random coil:24.0<br>
Turn:24.4<br>
</blockquote>
<br></div>
Have a look at the other output file do_dssp gives you.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
04 Ocak 2011 14:59 tarihinde Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> yazdı:<div class="im">
<br>
<br>
On 4/01/2011 11:38 PM, ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Mark,<br>
<br>
I will do by using the g_analyze tool but I do not know how to use it.<br>
</blockquote>
<br>
There's a section in Appendix D of the manual for each tool, or you<br>
can use the -h argument to the tool to get the same information.<br>
<br>
Either way, you haven't got the right tool. Hint: it's a "protein<br>
specific analysis"<br>
<br>
Mark<br>
<br>
<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
Thanks<br>
<br>
2011/1/4 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br></div>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><div class="im"><br>
<br>
On 4/01/2011 8:33 PM, ahmet yıldırım wrote:<br>
<br>
Hi,<br>
<br>
How can I calculate the percentages (alpha helix, beta<br>
sheet, coil ...) of secondary structure?<br>
<br>
<br>
Look in manual section 7.4 for a suitable tool.<br>
<br>
Mark<br>
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</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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